Variant report

Variant	rs7642643
Chromosome Location	chr3:100488975-100488976
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BRCA1	chr3:100488464-100488978	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:100477781..100481491-chr3:100485242..100489259,3	K562	blood:

Variant related genes	Relation type
ABI3BP	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12696195	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13069634	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs13089098	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13433770	0.85[AMR][1000 genomes]
rs1979895	0.92[CEU][hapmap]
rs6765500	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73861213	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7615467	1.00[CEU][hapmap];0.86[GIH][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs9814084	1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9823432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9836360	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9846590	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9873555	1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9877253	0.86[GIH][hapmap];0.83[TSI][hapmap]
rs9877951	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751972	chr3:100342493-100493062	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv432469	chr3:100342493-100493062	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7642643	GPR128	cis	multi-tissue	Pritchard
rs7642643	FAM55C	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100450000-100501000	Weak transcription	Esophagus	oesophagus
2	chr3:100467400-100497600	Weak transcription	Fetal Intestine Small	intestine
3	chr3:100469800-100498200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:100469800-100501400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:100470200-100498400	Weak transcription	Right Ventricle	heart
6	chr3:100471000-100495800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:100471600-100500400	Weak transcription	Lung	lung
8	chr3:100471800-100494600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:100471800-100502000	Weak transcription	Brain Anterior Caudate	brain
10	chr3:100472800-100494400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:100473600-100489200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr3:100473800-100496400	Weak transcription	Fetal Intestine Large	intestine
13	chr3:100474400-100494200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr3:100474400-100500200	Weak transcription	HSMM	muscle
15	chr3:100474400-100501200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr3:100475000-100499000	Weak transcription	Placenta	Placenta
17	chr3:100475600-100520000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr3:100478400-100496600	Weak transcription	Aorta	Aorta
19	chr3:100478800-100502000	Weak transcription	Psoas Muscle	Psoas
20	chr3:100479400-100493000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr3:100480200-100493800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:100486000-100489400	Weak transcription	Left Ventricle	heart
23	chr3:100487400-100490000	Strong transcription	Osteobl	bone
24	chr3:100487600-100489800	Strong transcription	NHDF-Ad	bronchial
25	chr3:100487600-100490000	Strong transcription	Stomach Smooth Muscle	stomach
26	chr3:100487800-100489800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:100488000-100489000	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr3:100488000-100489000	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr3:100488000-100489600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:100488200-100489000	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr3:100488200-100489200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
32	chr3:100488200-100489400	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr3:100488200-100490000	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr3:100488400-100489200	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr3:100488400-100490000	Strong transcription	Fetal Muscle Leg	muscle
36	chr3:100488600-100489000	Enhancers	Fetal Lung	lung
37	chr3:100488600-100489000	Enhancers	Gastric	stomach
38	chr3:100488600-100489800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:100488600-100489800	Strong transcription	Fetal Muscle Trunk	muscle
40	chr3:100488600-100489800	Strong transcription	Fetal Stomach	stomach
41	chr3:100488600-100489800	Strong transcription	Ovary	ovary
42	chr3:100488600-100490000	Strong transcription	Colon Smooth Muscle	Colon
43	chr3:100488600-100490000	Strong transcription	HSMMtube	muscle
44	chr3:100488600-100504600	Weak transcription	Adipose Nuclei	Adipose
45	chr3:100488800-100489000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr3:100488800-100489600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr3:100488800-100489600	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr3:100488800-100489800	Enhancers	H1 Cell Line	embryonic stem cell

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